Man pages for AllenInstitute/scrattch.hicat
Hierarchical Iterative Clustering Analysis for Transcriptomic data

calc_tauCalculate Tau scores for each gene
collect_co_matrixCollect co-clustering matrix from results files
collect_co_matrix_sparseMCollect coclustering results as a sparse matrix
compare_annotateCompare two sets of cluster assignments
convert_pair_matrixConvert paired cluster comparison values to a matrix
cpmConvert a matrix of count values to CPM (Counts per Million)
de_paramSet differential expression (DE) threshold for genes and...
de_scoreTitle cell co-clustering ratios
get_cl_matGenerate a sparse matrix one-hot representation of clusters x...
get_cl_meansCompute cluster means for each row in a matrix
get_cl_mediansCompute cluster medians for each row in a matrix
get_cl_sumsCompute cluster sums for each row in a matrix
get_eigenCompute module eigen genes
get_pair_matrixSubset a matrix as a vector using row and column positions
get_pair_matrix_coorConvert matrix row/column positions to vector position
iter_clustIterative clustering algorithm for single cell RNAseq dataset
iter_consensus_clustIterative consensus clustering
jaccardCompute jaccard distances between columns of a matrix
jaccard_louvainPerform Jaccard/Louvain clustering using Rphenograph
jaccard_louvain.FNNPerform Jaccard/Louvain clustering based on K-nearest...
map_by_corMap samples to a training dataset by correlation
map_cl_summaryMap a dataset to a reference, and compare existing cluster...
map_samplingPerform bootstrapped mapping using a fraction of provided...
merge_clMerge clusters based on pairwise differential expressed...
onestep_clustOne round of clustering in the iteractive clustering pipeline
reorder_clReorder cluster based on hiearchical clustering of clusters...
run_consensus_clustWrapper function to repeatively run clustering on subsampled...
sample_cellsDownsample cells from each cluster
sample_cells_by_genecountsSample cells from each cluster weighted by gene count
set_pair_matrixUpdate a matrix with values from a 1d vector using row and...
sparse_corCompute correlation scores for columns of a sparse matrix
AllenInstitute/scrattch.hicat documentation built on Feb. 26, 2019, 6:38 p.m.